To Linglingling,When you get to Aso station, a bus will take you up to a cablecar station (~45 minutes). At the cable car station, I'd recommend you walk up to the crater (~15-20 mintues along a road), rather than spend the money for a 5 min cablecar ride. This will also let you get some air and there's another path through Suna senri that you can walk for some different views.
To Annie D,
If you're on a JR pass while in Kyushu, then the Sun Q North pass doesn't pay off at all. It serves most of the same places as JR does (aside from Shimabara peninsula).
In terms of your itinerary, you should take a Ltd Express from Beppu to Aso as there are fewer trains directly between the two places. However, from Aso to Kumamoto, there is local service aside from Limited express trains. For example, there's an hourly local train from Aso to Higooza and then trains from Higooza to Kumamoto leave every 1/2 hr. Local trains will only cost you an extra 15 minutes or so.
On my trip, I travelled from Fukuoka to Nagasaki to Kumamoto to Aso to Beppu and back to Fukuoka on JR pass without any issues. Check Hyperdia for schedules:
http://grace.hyperdia.com/cgi-english/hyperWeb.cgi
-mike
